Re: [ccp4bb] odd waters

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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Subject: Re: odd waters
From: Abhinav Kumar abhinavk {- at -} SLAC {- dot -} STANFORD {- dot -} EDU
Date: 2008-05-27

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Subject: Re: odd waters
From: Bernhard Rupp bernhardrupp {- at -} SBCGLOBAL {- dot -} NET
Date: 2008-05-27

Dear All,

the consensus is that Cl- is most likely,
given the fact that backbone Ns and Arg
are involved in the contacts.

I think there is something wrong with my
surface calulation - need to check.

Thx! BR
_____

From: Petri Kursula [mailto:pkursula@sun3.oulu.fi]
Sent: Tuesday, May 27, 2008 9:38 PM
To: bernhardrupp@sbcglobal.net
Subject: [Bulk] Re: [ccp4bb] odd waters

From the coordination environment and distances, sure looks like a chloride
ion.
Petri

On May 28, 2008, at 4:38 AM, Bernhard Rupp wrote:

Dear All,

something one/some of you might have seen already and
might know what it might be/how to analyse:

Material: dimer of Se-Met, Ni-purified, NaCl and NaAc in
purification history.

I have 4 'waters', 2 each in the same monomer location
in a dimer of 2.5A Se-Met structure. They are multiple
coordinated - perhaps dist octahedron - and refine down to
B=2.0 and show correspondingly strong density. Surrounding
protein Bs range from 15 backbone to 37 Arg sidechain

First idea of course metal ions.
But the distances are odd - 3.1 to 3.7, unusually long for
common metal coordination.

If I use Na+/Mg++, the Bs still refine down to 4 to 6
K+ B's run up to ~25, Ni++ to 35-40, could be partial occ.

Given the charge distribution I doubt Cl- makes sense -
it sure looks like a nice place for cation. Not enough space
for sul- and fos-fates.

No experiments possible, have to deal with what's on hand.

Images on web:
http://www.ruppweb.org/images/snap.gif
http://www.ruppweb.org/images/mystery_ion.gif

How common are such large coordination distances in protein/metal
coordination and are there any (in silico) analysis tools one could use?

Thx, br
-----------------------------------------------------------------
Bernhard Rupp
001 (925) 209-7429
+43 (676) 571-0536
br@qedlife.com
bernhardrupp@sbcglobal.net
http://www.ruppweb.org/
-----------------------------------------------------------------
The hard part about playing chicken
is to know when to flinch
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---
Petri Kursula, Ph.D.
Academy Research Fellow
Docent of Neurobiochemistry
Department of Biochemistry
University of Oulu
Oulu, Finland
petri.kursula@oulu.fi
cc.oulu.fi/~pkursula
www.biochem.oulu.fi/kursula
---

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: odd waters
From: Abhinav Kumar abhinavk {- at -} SLAC {- dot -} STANFORD {- dot -} EDU
Date: 2008-05-27